The clock synchronization is the key technology in distributed control system. This paper investigates the method to adjust computer clock frequency and time in embedded control system based on Ethernet. This paper also analyses the basic working principle of the IEEE 1588 Precision Time Protocol. In particular, it outlines the working principle of the free PTPd that is the software only implementations of the IEEE 1588 Precision Time Protocol. In the ARM-Linux environment, it presents a clock synchronization method to achieve high precise clock synchronization in distributed control system using PTPd. The results indicate that it is able to synchronize distributed clocks with the accuracy less than 500 microseconds using PTPd without the support of specialized hardware.